How the attempt to sequence “Bigfoot’s genome” went badly off track

Humans interbred with an unknown hominin in Europe, then crossed the Bering Sea—say what?

When we first looked at the report of the bigfoot genome, it was an odd mixture of things: standard methods and reasonable looking data thrown in with unusual approaches and data that should have raised warning flags for any biologist. We just couldn't figure out the logic of why certain things were done or the reasoning behind some of the conclusions the authors reached. So, we spent some time working with the reported genome sequences themselves and talked with the woman who helped put the analysis together, Dr. Melba Ketchum. While it didn't answer all of our questions, it gave us a clearer picture of how the work came to be.

The biggest clarification made was what the team behind the results considered their scientific reasoning, which makes sense of how they ran past warning signs that they were badly off track. It provided an indication of what motivated them to push the results into a publication that they knew would cause them grief.

Melba Ketchum and the bigfoot genome

The public face of the bigfoot genome has been Melba Ketchum, a Texas-based forensic scientist. It was Ketchum who first announced that a genome was in the works, and she was the lead author of the paper that eventually described it. That paper became the one and only publication of the online journal De Novo; it's still the only one to appear there.

The paper itself is an odd mix of things. There's a variety of fairly standard molecular techniques mixed in with a bit of folklore and a link to a YouTube video that reportedly shows a sleeping Sasquatch. In some ways, the conclusions of the paper are even odder than the video. They suggest that bigfeet aren't actually an unidentified species of ape as you might have assumed. Instead, the paper claims that bigfeet are hybrids, the product of humans interbreeding with a still unknown species of hominin.

As evidence, it presents two genomes that purportedly came from bigfoot samples. The mitochondrial genome, a small loop of DNA that's inherited exclusively from mothers, is human. The nuclear genome, which they've only sequenced a small portion of, is a mix of human and other sequences. Some are closely related, others quite distant.

But my initial analysis suggested that the "genome sequence" was an artifact, the product of a combination of contamination, degradation, and poor assembly methods. And every other biologist I showed it to reached the same conclusion. Ketchum couldn't disagree more. "We've done everything in our power to make sure the paper was absolutely above-board and well done," she told Ars. "I don't know what else we could have done short of spending another few years working on the genome. But all we wanted to do was prove they existed, and I think we did that."

How do you get one group of people who looks at the evidence and sees contamination, while another decides "The data conclusively prove that the Sasquatch exists"? To find out, we went through the paper's data carefully, then talked to Ketchum to understand the reasoning behind the work.

Why they think it was genuine

Fundamentally, the scientific problems with the work seem to go back to the fact that some of the key steps—sample processing and preparation—were done by forensic scientists. As the name itself implies, forensic science is, like more general sciences, heavily focused on evidence, reproducibility, and other aspects shared with less applied sciences. But unlike genetics for example, forensic science is very goal-oriented. That seems to be what caused the problems here.

Over the decades that DNA has been used as forensic evidence, people in the field have come up with a variety of procedures that have been validated repeatedly. By following those procedures, they know the evidence they generate is likely to hold up in court. And, to an extent, it seems like the people behind the bigfoot genome wanted it to hold up in court.

“It's non-human hair—it's clearly non-human hair—it was washed and prepared forensically, and it gave a human mitochondrial DNA result. That just doesn't happen.”

Many of the samples they had were clumps of hair of various sizes. Hair is a common item in forensic analysis, where people have to identify whether the hair is human, whether it is a possible match for a suspect's, etc. In this case, the team was able to determine that the hair was not human. So far, so good.

In cases where the hair comes attached to its follicle, it's possible to extract DNA from its cells. And that is exactly what the bigfoot team did, using a standard forensic procedure that was meant to remove any other DNA that the hair had picked up in the interim. If everything worked as expected, the only DNA present should be from whatever organism the fur originated from.

And, in Ketchum's view, that's exactly what happened. They worked according to procedure, isolating DNA from the hair follicles and taking precautions to rule out contamination by DNA from anyone that was involved in the work. Because of this, Ketchum is confident that any DNA that came from the samples once belonged to whatever creature deposited the fur in the woods—no matter how confusing the results it produced were. "The mito [mitochondrial DNA results] should have done it," she argued. "It's non-human hair—it's clearly non-human hair—it was washed and prepared forensically, and it gave a human mitochondrial DNA result. That just doesn't happen."

Ketchum was completely adamant that contamination wasn't a possibility. "We had two different forensics labs extract these samples, and they all turned out non-contaminated, because forensics scientists are experts in contamination. We see it regularly, we know how to deal with mixtures, whether it's a mixture or a contaminated sample, and we certainly know how to find it. And these samples were clean."

But note the key phrase two paragraphs up: "if everything worked as expected." Anyone who's done much biology (or presumably, much science in general) knows that everything typically does not work as expected. In fact, things go badly wrong for all sorts of reasons. Sometimes it's obvious they went wrong, sometimes results look pretty reasonable but fall apart on careful examination.

In this case, there was no need for careful examination; the results the team got from the DNA was a mix of warning signs that things weren't right (internally inconsistent information) and things that simply didn't make any sense. But Ketchum believed so strongly in the rigor of the forensic procedures that she went with the results regardless of the problems. In fact, it seemed as if almost everything unusual about the samples was interpreted as a sign that there was something special about them.

146 Reader Comments

This is a wonderful write-up detailing one of the key aspects of science that is so often forgotten. (At least in my view, and Karl Popper's too), science isn't about gadgets or techniques or data ---- it's about the attempt to falsify hypotheses.

It looks like this team was so excited by an idea that they only believed the supporting evidence. Supporting evidence always exists, since so much data is essentially random, and Bayes' theorem only takes you so far. To be a good scientist, you need to keep an eye on the falsifying data.

I ended up building the bigfoot for the lead image by blending a capuchin monkey with a chimpanzee, with liberal clone tool fur and skin swapping. My first attempt used a human as the base, but if you saw it on Twitter I'm sure you'll agree it was way too disturbing to leave on the front page.

The public face of the bigfoot genome has been Melba Ketchum, a Texas-based forensic scientist. It was Ketchum who first announced that a genome was in the works, and she was the lead author of the paper that eventually described it. That paper became the one and only publication of the online journal De Novo; it's still the only one to appear there.

...

For some unfathomable reason, team bigfoot didn't use it. Instead, they took a single human chromosome and got some software to line up as much as it could to that.

So team Ketchum published a paper in a journal called De Novo, but failed to use a de novo assembler.

.. Well, You know ... It does kinda fit in with all the aquatic ape stuff, ... And as its been well established 'long-pig' or human when cooked does have the distinctive odor of bacon, and as various animal trainers have told me pigs favorite food is bacon, they will do anything for it .. And my favorite food is bacon ... I will almost do anything for it, so Therefore .. It must be true.

"Instead, each sample tested produced a different mitochondrial DNA sequence, which implies the interbreeding had to have taken place many, many times."

And as far as I can see it also implies, if the sample was taken from one individual, that the single egg cell from which that individual developed must have contained many mitochondria with wildly varying genomes, within that one cell. I know there can be some variation from mitochondrion to mitochondrion within a cell, but I don't see how the variations would be that numerous and extensive.

I tried to find information about the diversity of mitochondria genomes within a single cell, and couldn't find much, but apparently small variations do happen and are the source of variable inheritance of mitochondrial diseases.

So, another point against their analysis.

edit: oops, just saw that the sample did come from multiple individuals. But how many? There is still only so much mitochondrial variation you would see from a few individuals of the same species.

.. Well, You know ... It does kinda fit in with all the aquatic ape stuff, ... And as its been well established 'long-pig' or human when cooked does have the distinctive odor of bacon, and as various animal trainers have told me pigs favorite food is bacon, they will do anything for it .. And my favorite food is bacon ... I will almost do anything for it, so Therefore .. It must be true.

Two points I want to make: The first is that PCR doesn't necessarily rely on human DNA sequences, as you said. Second is that I can say one very good reason they didn't send this for high thoroughput sequencing right now: it costs a lot of time and money. A LOT of time and money. Then again, idk how well funded this lab is.

Good writeup, John! But just a small nitpick about the NGS data (top of page 3): nowadays because we have so many reference genomes, resequencing (sequencing by alignment) is the standard procedure even for unknown organisms. The assembly procedure into contigs is usually done afterward for non-aligning reads. So, their approach appears to be good, but like you said, their non-aligning reads afterward (you said >100bp, so I'm guessing they were assembled after the fact) showed a bunch of different organisms. That should have been their major red flag.

It appears that their approach and protocols used were standard in their respective fields, but they lacked serious critical thinking in how to interpret their results. Just because you followed the protocols step by step doesn't mean the results are golden. They also didn't think critically about their sample source too -- one critical related study is Paabo and colleagues who study Neanderthal and Denisovan genomes. They systematically rule out contamination and are very careful about the sources of their samples. It's amazing that this scientist did not even do her due diligence in that regard.

But note the key phrase two paragraphs up: "if everything worked as expected." Anyone who's done much biology (or presumably, much science in general) knows that everything typically does not work as expected.

(emphasis added)

That pretty much sums up my entire PhD (and, I'm sure, many other peoples' too!)

So the lead researcher knows a place where you can go and look at living, breathing Sasquatch but has chosen to prove their existence by performing DNA testing on some hair found in the woods? Next she will prove that elephants exist by DNA testing on dung from the local zoo.

This is a wonderful write-up detailing one of the key aspects of science that is so often forgotten. (At least in my view, and Karl Popper's too), science isn't about gadgets or techniques or data ---- it's about the attempt to falsify hypotheses.

And it also shows something everyone would like to forget about. Science is, ultimately, done by people. Smart, prideful, jealous, compassionate, hopeful, fallible people. You don't start months and thousands of dollars of research thinking, "Boy, I sure hope I'm wrong about this hypothesis!" It's when we let those innate qualities that make us human override those gadgets, techniques, and data that we run into situations like this, and Piltdown Man, and cold fusion, etc, etc. Failures such as these don't cause me to despair the state of things. The opposite in fact. They remind us that science is the art of questioning. And yes, I said art. Deal with it :-) Question can there really be a Bigfoot? Question the results either way vigorously. Question gadgets and techniques and data and motives. Science will truly only fail when the failures and quasi-hoaxes stop. That would mean we've stopped asking the hard, uncomfortable questions that NEED to be asked and have fallen into and wallow in a pit of self-satisfaction, certainty, and ultimately oblivion.

... They suggest that bigfeet aren't actually an unidentified species of ape as you might have assumed. Instead, the paper claims that bigfeet are hybrids, the product of humans interbreeding with a still unknown species of hominin.

Are humans no longer classified as apes? I thought ape was synonym for hominoidea.

you know that feeling you get when you're watching someone perform live and they're totally bombing but trying to push through anyways; that embarrassed kind of feeling where you want to turn away. i felt that while reading this whole article.

I find it very hard to believe that a large hominid lives in North America and had never, ever left any solid proof. No animals, bones, hair, clear pictures, solid videos, or anything else. I would even conjecture (as many respected scientists have) that such a thing is totally impossible.

Because of this, I find it hard to take anything anyone takes seriously if they mention Bigfoot in anything but the fictional sense. You've been very nice to take this TOTALLY INSANE KOOK seriously but it's hard to believe that anyone could possibly take these insane rantings seriously.

I am certainly no genetic scientist and might be talking nonsense here but … I've always wondered why the problem isn't approached from the point of view of what Sasquatch *could* be rather than searching for evidence of this type that usually turns out to come from some trailer park in Arkansas.

By that I mean that the descriptions of Sasquatch are fairly consistent even down to behaviour and diet and that such a creature *did* actually exist at one time. Namely Australopitcethus Robustus. This is a real creature that existed that matches the description in pretty much every single way. It was a gigantic, vegetarian, hairy primate with big feet that walked upright like a human in the same time period as homo erectus.

Since A. Robustus lived not that long ago it's unlikely that "Sasquatch" (if it exists at all) is an entirely different creature. The only way Sasquatch can really be real is if it is some kind of remnant of this same creature.

We have A. Robustus bones, and while we don't have DNA we have a pretty good idea about where it sits in the human family tree. Why not focus exclusively on whether the two could possibly be the same and analyse the supposed Sasquatch DNA from that viewpoint?

Personally, I don't think Sasquatch is real at all, but if it is, the number of things it could be is really very limited. A. Robustus is almost the only thing we know about that matches at all.

There is probably more than just confirmation bias at play here (though that is likely there too -she does seem like a true 'bleever). Reports are around that Ketchum has collected around $450,000 from ONE backer of her project.

The backstory for the 'novel hominin' that interbred 'no more than 13,000 years ago' with humans is Nephilim. Yes she believes that the biblical Nephilim interbred with human females (as per the bible), and produced bigfoots.

Ketchum and (her co-..something) Paulides are now moving into ancient alien territory with dna testing of skulls. Much more money in aliens than bigfoot probably -and if you can merge the fields? Gold mine.